Dear SCT team!
I have a problem with SCT installation (with the new version 5 and also with older versions) using MacOS 10.15.6. It says “Problem creating launchers!”. Do you think there is a problem with python?
I attached the terminal output of install_sct and sct_check_dependencies…
install_sct.txt (34.9 KB) sct_check_dependencies.txt (3.7 KB)
Thank you for your help!
Best,
Britta
Hi Britta,
Welcome to the forum, and thank you for reporting your issue. 
It looks like there may have been a clash with an existing 4.2.2 installation of SCT.
To start fresh, could you please try deleting the existing installation folder (/Users/macpronirims/sct_5.0.0/) and after that try re-running the 5.0.0 installation script?(/Users/macpronirims/Downloads/spinalcordtoolbox-5.0.0/install_sct)
Thank you kindly,
Joshua
Hi Joshua,
after deleting the installation folder I’ve received the same output: install_sct.txt (28.2 KB)
Thank you!
Britta
Hi Britta,
The SCT developer team is actively investigating your issue. Thank you for your patience.
I’d like to try and learn a bit more about what’s happening in your system. Could you please run the following commands in your terminal?
cd /Users/macpronirims/sct_5.0.0/
source python/etc/profile.d/conda.sh
conda activate venv_sct
Your terminal should change to show the text “(venv_sct)”. I’ll demonstrate using my own system:
joshua@pop-os:~$ cd sct_5.0.0/
joshua@pop-os:~/sct_5.0.0$ source python/etc/profile.d/conda.sh
joshua@pop-os:~/sct_5.0.0$ conda activate venv_sct
(venv_sct) joshua@pop-os:~/sct_5.0.0$
But if something else happens, please let us know.
Thank you kindly,
Joshua
Hi Joshua,
Sorry for my late reply. I’ve got the same terminal output as you…
Thank you
Britta
Hi Britta,
Upon closer inspection, I believe the issue is due to the presence of pyenv on your system.
Normally, SCT would get installed to its own Python version, which is stored inside the “/Users/macpronirims/sct_5.0.0/python” folder. But, I believe pyenv is intercepting this installation, causing SCT to instead be installed to “/Users/macpronirims/.pyenv/versions/3.6.9”.
We are currently looking into a solution to prevent pyenv from interfering. You can track the progress here. 
Thank you for your patience as we work to address this!
Kindly,
Joshua
Hi Britta,
Could you please run the following commands and share the output?
which python
which pip
source $SCT_DIR/python/etc/profile.d/conda.sh
conda activate venv_sct
which python
which pip
Thank you kindly,
Joshua
Hi Joshua,
this is the output:
(base) MACpros-Mac-Pro:~ macpronirims$ which python
/Users/macpronirims/.pyenv/shims/python
(base) MACpros-Mac-Pro:~ macpronirims$ which pip
/Users/macpronirims/.pyenv/shims/pip
(base) MACpros-Mac-Pro:~ macpronirims$ source sct_5.0.0/python/etc/profile.d/conda.sh
(base) MACpros-Mac-Pro:~ macpronirims$ conda activate venv_sct
(venv_sct) MACpros-Mac-Pro:~ macpronirims$ which python
/Users/macpronirims/.pyenv/shims/python
(venv_sct) MACpros-Mac-Pro:~ macpronirims$ which pip
/Users/macpronirims/.pyenv/shims/pip
Thank you for sharing the output; it definitely demonstrates the issue. On my computer, here is what I see:
joshua@XPS-15-9560:~$ which python
/home/joshua/.pyenv/shims/python
joshua@XPS-15-9560:~$ which pip
/home/joshua/.pyenv/shims/pip
joshua@XPS-15-9560:~$ source $SCT_DIR/python/etc/profile.d/conda.sh
joshua@XPS-15-9560:~$ conda activate venv_sct
(venv_sct) joshua@XPS-15-9560:~$ which python
/home/joshua/sct_5.0.1/python/envs/venv_sct/bin/python
(venv_sct) joshua@XPS-15-9560:~$ which pip
/home/joshua/sct_5.0.1/python/envs/venv_sct/bin/pip
The above shows that the python/pip executables should switch from the “pyenv” versions to the ones used by SCT. But, for your system, nothing changes, which is very peculiar.
I’ll continue to look into why this is happening and what we can do about it.
Kind regards,
Joshua
Hi Britta,
Could you please run the following commands and share the output?
source $SCT_DIR/python/etc/profile.d/conda.sh
conda activate venv_sct
conda info
conda config --show-sources
conda list --show-channel-urls
Thank you,
Joshua
Hi Joshua,
Thank you very much for your effort. This is my output:
(base) MACpros-Mac-Pro:~ macpronirims$ source sct_5.0.0/python/etc/profile.d/conda.sh
(base) MACpros-Mac-Pro:~ macpronirims$ conda activate venv_sct
(venv_sct) MACpros-Mac-Pro:~ macpronirims$ conda info
active environment : venv_sct
active env location : /Users/macpronirims/sct_5.0.0/python/envs/venv_sct
shell level : 2
user config file : /Users/macpronirims/.condarc
populated config files :
conda version : 4.8.3
conda-build version : not installed
python version : 3.8.3.final.0
virtual packages : __osx=10.15.6
base environment : /Users/macpronirims/sct_5.0.0/python (writable)
channel URLs : https://repo.anaconda.com/pkgs/main/osx-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/osx-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /Users/macpronirims/sct_5.0.0/python/pkgs
/Users/macpronirims/.conda/pkgs
envs directories : /Users/macpronirims/sct_5.0.0/python/envs
/Users/macpronirims/.conda/envs
platform : osx-64
user-agent : conda/4.8.3 requests/2.23.0 CPython/3.8.3 Darwin/19.6.0 OSX/10.15.6
UID:GID : 501:20
netrc file : None
offline mode : False
(venv_sct) MACpros-Mac-Pro:~ macpronirims$ conda config --show-sources
(venv_sct) MACpros-Mac-Pro:~ macpronirims$ conda list --show-channel-urls
# packages in environment at /Users/macpronirims/sct_5.0.0/python/envs/venv_sct:
#
# Name Version Build Channel
ca-certificates 2020.10.14 0 defaults
certifi 2020.6.20 pyhd3eb1b0_3 defaults
libcxx 10.0.0 1 defaults
libedit 3.1.20191231 h1de35cc_1 defaults
libffi 3.3 hb1e8313_2 defaults
ncurses 6.2 h0a44026_1 defaults
openssl 1.1.1h haf1e3a3_0 defaults
pip 20.2.4 py36hecd8cb5_0 defaults
python 3.6.12 h26836e1_2 defaults
readline 8.0 h1de35cc_0 defaults
setuptools 50.3.1 py36hecd8cb5_1 defaults
sqlite 3.33.0 hffcf06c_0 defaults
tk 8.6.10 hb0a8c7a_0 defaults
wheel 0.35.1 py_0 defaults
xz 5.2.5 h1de35cc_0 defaults
zlib 1.2.11 h1de35cc_3 defaultsHi @BrMa. Thank you for waiting. We have been able to pinpoint the cause of your issue. It is due to a complicated interaction between:
pyenv (already on your system)(base) conda environment (already on your system)(venv_sct) conda environmentWe also believe we have found a simple fix for your issue. Could you please run “conda deactivate” before installing SCT?
conda deactivate
./install_sct
The “(base)” prefix on your terminal should go away before SCT is installed.
Kind regards,
Joshua
Hi Joshua,
Great, it worked! Thank you very much for your help.
Best regards,
Britta
I’m glad to hear that!
One last note: I notice in this comment of yours that even though the (base) environment looks active, the pyenv Python gets used instead of the (base) conda’s Python. So, it could be beneficial for you to disable the base environment in fresh terminals if you’re not using it, which could help prevent conflicts like this in the future.
Otherwise, I hope you enjoy using SCT! And, feel free to use the forum for any other questions or concerns you may have.
Kind regards,
Joshua